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The Journal of Open Source Software (JOSS): Bringing Open-Source Software Practices to the Scholarly Publishing Community for Authors, Reviewers, Editors, and Publishers

Open-source software (OSS) is a critical component of open science, but contributions to the OSS ecosystem are systematically undervalued in the current academic system. The Journal of Open Source Software (JOSS) contributes to addressing this by providing a venue (that is itself free, diamond open access, and all open-source, built in a layered structure using widely available elements/services of the scholarly publishing ecosystem) for publishing OSS, run in the style of OSS itself. A particularly distinctive element of JOSS is that it uses open peer review in a collaborative, iterative format, unlike most publishers. Additionally, all the components of the process—from the reviews to the papers to the software that is the subject of the papers to the software that the journal runs—are open. We describe JOSS’s history and its peer review process using an editorial bot, and we present statistics gathered from JOSS’s public review history on GitHub showing an increasing number of peer reviewed papers each year. We discuss the new JOSSCast and use it as a data source to understand reasons why interviewed authors decided to publish in JOSS. JOSS’s process differs significantly from traditional journals, which has impeded JOSS’s inclusion in indexing services such as Web of Science. In turn, this discourages researchers within certain academic systems, such as Italy’s, which emphasize the importance of Web of Science and/or Scopus indexing for grant applications and promotions. JOSS is a fully diamond open-access journal with a cost of around US$\$$5 per paper for the 401 papers published in 2023. The scalability of running JOSS with volunteers and financing JOSS with grants and donations is discussed.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION

PSCF+: An Extended and Improved Open-Source Software Package for Polymer Self-Consistent Field Calculations

This work introduces PSCF+, a freely available open‑source software tool for modeling how block copolymers self‑assemble into ordered nanoscale structures. The software allows researchers to study a wide range of polymer models and interaction types, making it possible to directly compare theoretical predictions with molecular and simulation‑based studies in a consistent way. PSCF+ incorporates several recently developed numerical methods that significantly reduce computer memory requirements and speed up calculations, enabling efficient use of modern GPU hardware. Here, it also provides automated tools to calculate free‑energy landscapes and phase boundaries, which are essential for understanding and predicting material behavior. Together, these advances make PSCF+ a powerful and flexible platform for studying polymer self‑assembly and support the design of new polymeric materials for scientific and technological applications.

Chemical calculations

JUSTIFI: Open-Source Software for Identifying and Quantifying Non-Energy Benefits

The integration of Non-Energy Benefits (NEBs) into energy efficiency initiatives is essential for operational excellence in manufacturing. This presentation and software demonstration explore how quantifying NEBs such as improved safety, increased quality, and enhanced productivity, can strengthen business cases for energy investments, leading to better payback periods and alignment with organizational goals. We introduce JUSTIFI, a free, open-source software by the U.S. Department of Energy that aids in the measurement of NEBs and enhances understanding of their impact on Key Performance Indicators (KPIs) and return on investment (ROI). JUSTIFI features an intuitive interface for identifying NEBs, customizable reporting tools, and comprehensive system cataloging, empowering companies to effectively communicate the value of energy efficiency projects. By leveraging this innovative tool, organizations can better navigate energy efficiency assessments and drive support for their energy management initiatives.

29 ENERGY PLANNING, POLICY, AND ECONOMY

Improving Performance via Energy Efficiency JUSTIFI: Open-Source Software for Identifying and Quantifying Non-Energy Benefits

Energy efficiency is pivotal to achieving operational excellence, as it enhances value while reducing waste. This presentation explores the integration of non-energy benefits (NEBs) into energy efficiency projects, which can lead to risk reduction, value creation, and cost savings. By quantifying NEBs - such as improved safety, decreased pollution, and increased productivity - companies can strengthen their business cases for energy investments, ultimately improving payback periods and aligning with strategic goals. Designed for a diverse audience, from trained auditors to novices in energy assessments, we have developed open-source software called JUSTIFI, NEB finding methodology, and training materials which build on existing frameworks and leverages resources from the U.S. Department of Energy and Better Plants energy system analysis software suite such as MEASUR. This work aims to maximize ROI through NEB identification, utilizing tools like JUSTIFI and the NEBs Discovery Protocol.

97 MATHEMATICS AND COMPUTING

Scientific Open-Source Software Is Less Likely to Become Abandoned Than One Might Think! Lessons from Curating a Catalog of Maintained Scientific Software

Scientific software is essential to scientific innovation and in many ways it is distinct from other types of software. Abandoned (or unmaintained), buggy, and hard to use software, a perception often associated with scientific software can hinder scientific progress, yet, in contrast to other types of software, its longevity is poorly understood. Existing data curation efforts are fragmented by science domain and/or are small in scale and lack key attributes. We use large language models to classify public software repositories in World of Code into distinct scientific domains and layers of the software stack, curating a large and diverse collection of over 18,000 scientific software projects. Using this data, we estimate survival models to understand how the domain, infrastructural layer, and other attributes of scientific software affect its longevity. We further obtain a matched sample of non-scientific software repositories and investigate the differences. We find that infrastructural layers, downstream dependencies, mentions of publications, and participants from government are associated with a longer lifespan, while newer projects with participants from academia had shorter lifespan. Against common expectations, scientific projects have a longer lifetime than matched non-scientific open-source software projects. We expect our curated attribute-rich collection to support future research on scientific software and provide insights that may help extend longevity of both scientific and other projects.

Malviya Thakur, Addi [ORNL] (ORCID:000000022681999

Lessons Learned from Open-Source Software Training Toward Expanding the Fusion Workforce

Within the United States (U.S.), the Fusion Innovation Research Engine (FIRE) Collaboratives seek to accelerate fusion technology development through wide-ranging community-driven research activities that bring together industry, laboratories, research institutes, and academia. Increasing the maturity of key components and systems for future fusion power plants (FPPs) toward commercialization, will, by necessity, increase the need for knowledgeable engineers, designers, and researchers in industry capable of integrating and further improving these technologies within industry FPP concepts. Further, various modeling and simulation packages support these programs and are under-development within them to drive design iteration and the development of FPP digital twins. To derive the greatest benefit from model output and capabilities, training these same specialists will be vital. Thus, the development of effective and accessible software onboarding and professional development opportunities focused on fusion will be key to keeping the pace of growth high in the coming decade and beyond. A similar need exists within the advanced fission reactor community, driven by an ever-growing need for carbon-free baseload power for industrial and data center applications. Within the U.S. and around the world, several open-source packages and frameworks exist to support this endeavor, and two we will highlight here are the Multiphysics Object Oriented Simulation Environment (MOOSE) framework and OpenMC. These packages, notably, are also being utilized in the FIRE Collaboratives program. In this presentation, we will highlight the lessons learned from over 30 years of combined software development and training experience, focused on developing strong technical software foundations within the nuclear workforce, from students to professional engineers & scientists. We will connect this experience to present and emerging needs in the fusion energy community, and, finally, will outline possible paths forward to develop a large, robust, global fusion workforce.

70 - PLASMA PHYSICS AND FUSION TECHNOLOGY

geoPFA: A Python-Based Open-Source Software for 3D Geothermal PFA

This work presents a novel Python-based framework, geoPFA, for conducting 3D play fairway analysis (PFA) tailored to superhot geothermal systems. The workflow has been applied to the Nesjavellir field in Iceland, a candidate site for the third Iceland Deep Drilling Project's superhot production scenarios. This application demonstrates the value of modular, transparent, and extensible workflows for integrating geological, geophysical, and simulation-derived datasets in high-enthalpy environments. Preliminary results indicate favorable zones consistent with known hydrothermal activity. The geoPFA library will soon be publicly available, offering a scalable and reproducible approach to geothermal exploration across varied geological contexts.

15 GEOTHERMAL ENERGY

Open Source Software Prevalence Ingest Tool

The OSSP Ingest Tool accepts user-input organizational information, ingests IT/OT asset lists in Excel format, and ingests the associated CycloneDX SBOM's. It then performs analytics demonstrating the ability to answer the follow research questions: o RQ1. Ability to identify all OSS services running on, and all OSS components present within, an OT device o RQ1a: Ability to differentiate multiple versions of the same OSS component within each OT device. o RQ1b: Ability to differentiate running from not-running OSS components. o RQ1c: Ability to differentiate based on the originator of the component, because a supplier may have modified it after retrieval from the upstream software source. o RQ2. Ability to correlate the identity of a single OSS component across multiple OT devices, mitigating common name variations such as differences in capitalization, '-' vs '_', and so on. o RQ3. Ability to perform subset analysis of OSS components across multiple OT devices o RQ3a: Ability to perform subset analysis across OSS libraries, generating density & distribution graphs to identify commonly-used libraries and outliers. o RQ3b: Ability to perform subset analysis of a single OSS library, generating density & distribution by CI sector, by device type, by device make/model, and/or by firmware version. o RQ3c: Ability to perform subset analysis by grouping OSS libraries according to programming language, then overlay with RQ4b. o RQ3d: Ability to perform subset analysis by OSS upstream source, providing insight into degree of modifications performed by suppliers. o RQ4. Ability to identify dependencies (transitive and direct) of each differentiated OSS library within each OT device, and enable RQ1,2,3 iteratively for dependencies. o RQ1. Ability to identify all OSS services running on, and all OSS components present within, an OT device o RQ1a: Ability to differentiate multiple versions of the same OSS component within each OT device. o RQ1b: Ability Page

Kapadia, Shayna [Lawrence Livermore National Labor

MPACT Safeguards Modeling: FY25 Update

Sandia National Laboratories develops and maintains several open-source software packages to support material accountancy analyses. This includes the Material Accountancy Performance Indicator Toolkit (MAPIT), the Fissile Facility Flow Modeler (F3M) and the Separation and Safeguards Performance Model Library (SSPM-L). MAPIT is responsible for performing statistical safeguards analyses on bulk and itemized data from nuclear fuel cycle facilities and can operate on real or synthetic data. MAPIT is the only open-source software for such analyses. F3M is a library of modules, built in MATLAB Simulink, that contain pre made blocks to represent different generic fuel cycle processes. These blocks can be used together in a modular fashion to represent and simulate nuclear fuel cycle processes with the goal of improving facility-level accountancy during the design phase. F3M is also an open-source library. Finally, the SSPM-L library is a series of completed models built from F3M. The library includes facility models such as a generic PUREX facility and a fuel fabrication facility. The SSPM-L library is not open source, but is available to collaborators with a relevant use case. These tools include modeling and simulation pipelines to simulate nuclear fuel cycle facilities and the underlying software needed to simulate measurement uncertainty and perform statistical analyses. Together, these tools can perform end-to-end nuclear material accountancy analyses. This report documents the various improvements made to these tools in FY25. Specifically, we added new statistical test, new statistical modeling capabilities, new fuel cycle facility models, and launched a new open-source model component library.

97 MATHEMATICS AND COMPUTING

Multiscale Nuclear-Electronic Orbital Quantum Dynamics in Complex Environments

Many renewable energy conversion processes rely on the movement of protons as well as electrons through either electrocatalysis or photoexcitation. The simulation of such processes requires a quantum mechanical description of coupled nuclear-electronic dynamics in a solvent or heterogeneous chemical environment. The overall objective of this project is the development of theoretical and computational capabilities for simulating nuclear-electronic quantum dynamics in complex environments and the creation of high-performance, open-source software. This multiscale framework will enable simulations of the real-time dynamics of nonequilibrium excited state proton-coupled electron transfer, quantum decoherence, vibronic energy transfer, and ultrafast radiolysis, as well as their associated time-resolved multidimensional spectroscopies. An important outcome of this project will be a sustainable, reusable, and interoperable open-source software ecosystem. This software will be designed for emerging exascale and future national leadership computers. Another key outcome will be a multiscale quantum dynamics method and software enabling simulations of nonequilibrium nuclear-electronic quantum dynamics in complex environments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC

Recent Developments in DFTB+, a Software Package for Efficient Atomistic Quantum Mechanical Simulations

DFTB+ is a flexible, open-source software package developed by its community, designed for fast and efficient atomistic quantum mechanical simulations. It employs various methods that approximate density functional theory (DFT), such as density functional-based tight binding (DFTB) and the extended tight binding (xTB) approach allowing simulations of large systems over extended time scales with reasonable accuracy, while being significantly faster than traditional ab initio methods. In recent years, several new extensions of the DFTB method have been developed and implemented in the DFTB+ program package in order to improve the accuracy and generality of the available simulation results. In this paper, we review those enhancements, show several use case examples and discuss the strengths and limitations of its features.

36 MATERIALS SCIENCE

A Million Person Study Innovation: Evaluating Cognitive Impairment and other Morbidity Outcomes from Chronic Radiation Exposure Through Linkages with the Centers for Medicaid and Medicare Services Assessment and Claims Data

Here, the study of One Million U.S. Radiation Workers and Veterans, the Million Person Study (MPS), examines the health consequences, both cancer and non-cancer, of exposure to ionizing radiation received gradually over time. Recently the MPS has focused on mortality patterns from neurological and behavioral conditions, e.g., Parkinson's disease, Alzheimer's disease, dementia, and motor neuron disease such as amyotrophic lateral sclerosis. A fuller picture of radiation-related late effects comes from studying both mortality and the occurrence (incidence) of conditions not leading to death. Accordingly, the MPS is identifying neurocognitive diagnoses from fee-for-service insurance claims from the Centers for Medicare and Medicaid Services (CMS), among Medicare beneficiaries beginning in 1999 (the earliest date claims data are available). Linkages to date have identified ∼540,000 workers with available health information. Such linkages provide individual information on important co-factor and confounding variables such as smoking, alcohol consumption, blood pressure, obesity, diabetes and many other health and demographic characteristics. The total person-level set of time-dependent variables, outcomes, organ-specific dose measures, co-factors, and demographics will be massive and much too large to be evaluated with standard software. Thus, development of specialized open-source software designed for large datasets (Colossus) is nearly complete. The wealth of information available from CMS claims data, coupled with individual dose reconstructions, will thus greatly enhance the quality and precision of health evaluations for this new field of low-dose radiation and neurocognitive effects.

Dauer, Lawrence T.

MFC 5.0: An exascale many-physics flow solver

Many problems of interest in engineering, medicine, and the fundamental sciences rely on high-fidelity flow simulation, making performant computational fluid dynamics solvers a mainstay of the open-source software community. Previous work MFC 3.0 was made a published, documented, and open-source solver via Bryngelson et al. Comp. Phys. Comm. (2021) with numerous physical features, numerical methods, and scalable infrastructure. MFC 5.0 is a significant update to MFC 3.0, featuring a broad set of well-established and novel physical models and numerical methods, as well as the introduction of GPU and APU (or superchip) acceleration. Here, we exhibit state-of-the-art performance and ideal scaling on the first two exascale supercomputers, OLCF Frontier and LLNL El Capitan. Combined with MFC’s single-accelerator performance, MFC achieves exascale computation in practice, and achieved the largest-to-date public CFD simulation at 200 trillion grid points as a 2025 ACM Gordon Bell Prize finalist. New physical features include the immersed boundary method, N-fluid phase change, Euler–Euler and Euler–Lagrange sub-grid bubble models, fluid-structure interaction, hypo- and hyper-elastic materials, chemically reacting flow, two-material surface tension, magnetohydrodynamics (MHD), and more. Numerical techniques now represent the current state-of-the-art, including general relaxation characteristic boundary conditions, WENO variants, Strang splitting for stiff sub-grid flow features, and low Mach number treatments. Weak scaling to tens of thousands of GPUs on OLCF Summit and Frontier and LLNL El Capitan achieves efficiencies within 5% of ideal to over 90% of their respective system sizes. Strong scaling results for a 16-times increase in device count show parallel efficiencies over 90% on OLCF Frontier. MFC’s software stack has undergone further improvements, including continuous integration, which ensures code resilience and correctness through over 300 regression tests; metaprogramming, which reduces code length while maintaining performance portability; and code generation for computing chemical reactions

Computational fluid dynamics

Tough Errors Are no Match (TEAM): Optimizing the quantum compiler for noise resilience

This report summarizes Unitary Fund’s contributions to the Department of Energy’s TEAM project (DE-SC0020266) under Thrust 2: Quantum Programming and Compilation. The central outcomes of this work have been the development of Mitiq, an open-source Python toolkit for applying quantum error mitigation (QEM) techniques to noisy quantum programs, and the invention, benchmarking and theoretical investigation of novel QEM techniques. Additional outcomes include the development of other open source software packages for the usage, simulation and control of quantum computers.

97 MATHEMATICS AND COMPUTING

From Modular ADMS to Plug-and-Play Ops: Distribution Grid Operations with Platform-Level Orchestration to Enable Ambitious App Hosting

The core function of the distribution grid is to provide electricity to consumers affordably, reliably, and securely. In pursuing these core objectives, distribution utilities are accountable to customers, regulators, and in some cases, shareholders. Other third parties such as aggregators and microgrids can also have a stake in the smooth operation of the grid. Each of these stakeholders has economic, business, and/or governance objectives that inform their expectations of the distribution grid. This multi-objective, multi-stakeholder environment creates tension that must be reconciled to successfully design and operate the distribution grid. Innovative companies are competing to bring high-tech solutions to electric utilities and their customers that address each of these objectives. Many developers of advanced distribution management systems (ADMS) and distributed energy resource management systems (DERMS) have adopted a modular architecture that allows grid operators to select functions and features according to their individual system needs. A modular platform also allows the solution provider to develop and integrate specific new product modules; however, the need to pursue multiple objectives with a fixed set of controllable devices makes integration expensive whether it is done at the product development stage or the deployment stage. This cost creates a significant barrier to adoption and can lengthen the product to market time of new solutions. To fundamentally address the complexity of system integration for distribution grid operations, the U.S. Department of Energy Office of Electricity has funded the GridAPPS-D project at PNNL, which streamlines integration by contributing to standards development, defining system architecture, applying advanced mathematics, and developing open-source software to demonstrate the concept of an open data-integration platform for distribution operations. The open data-integration platform concept enables system operators and solution providers to deploy ambitious, best-of-breed applications (or apps) without continually reengineering for integration. Ambitious apps developed by different solution providers will inevitably attempt to achieve different control objectives with the same set of controllable devices. If the open platform itself can resolve these conflicts in a way that achieves the best available outcomes for all apps, doesn’t restrict the ambitious design of apps, and ensures safe and secure operations, apps will be able to plug-and-play with the platform at the same time as other ambitious apps. In this paper, we describe a framework called App Deconfliction that empowers a platform to assign setpoints to controllable devices based on the values preferred by different apps (and even external stakeholder entities like customers or aggregators). The App Deconfliction framework is compatible with several methods for determining setpoint values. We present two methods based on game theory that provide a subtle built-in incentive structure for developers to adapt their apps to the fact that they will be operating in a moderated multi-app environment and to favor device setpoints that have the most effect on their objectives over those that have the least effect. Our simulation-based demonstrations have shown that game-theory-based deconfliction can lead to a 7% improvement in control space utilization compared to design-based methods.

24 POWER TRANSMISSION AND DISTRIBUTION

Exploring Sustainability in Scientific Software through Code Quality & Test Coverage Metrics

Context: Scientific open-source software (SciOSS) plays a foundational role in research and engineering, yet its long-term sustainability has often been overlooked and remains a significant concern. Objective: This study investigates the long-term sustainability of SciOSS through code and test quality metrics. Method: We analyze CASS Software Portfolio projects, classifying them by sustainability and comparing their code structure, test coverage, and links between code quality and testing across the dataset. Results: Sustainable projects show higher, more consistent test coverage and clearer code-test correlations, while unsustainable ones show weaker patterns. Overall, test coverage is low in scientific software, and high complexity and coupling reduce testability. Conclusion: In this study, we present a practical, data-driven approach for assessing sustainability in scientific software, offering a foundation for evaluating long-term software health and supporting future efforts in quality assurance and sustainability monitoring.

Md mushfiqur rahman, Sheikh [University of Tenness